Detailed view for PF3D7_0607300

Basic information

TDR Targets ID: 4427
Plasmodium falciparum, uroporphyrinogen III decarboxylase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.9062 | Length (AA): 413 | MW (Da): 48833 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 2

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF01208   Uroporphyrinogen decarboxylase (URO-D)

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0004853   uroporphyrinogen decarboxylase activity  
GO:0006779   porphyrin biosynthetic process  

Structural information

Modbase 3D models:

There are 6 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
58 412 1r3s (A) 11 362 30.00 0 1 1.45 -2.44
83 410 1r3s (A) 32 360 31.00 0 1 1.42 -2.65
58 412 1r3s (A) 11 362 30.00 0 1 1.32596 -1.3
59 413 4exq (A) 3 357 28.00 0 1 1.28396 -1.28
60 411 4zr8 (A) 3 352 31.00 0 1 1.3151 -1.2
62 412 1j93 (A) 10 352 29.00 0 1 1.20868 -0.97

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Oocyst, Male Gametocyte. Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Female Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 40 hs, Ring. Otto TD Zanghi G
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127347)

Species Accession Gene Product
Arabidopsis thaliana AT2G40490   Uroporphyrinogen decarboxylase
Arabidopsis thaliana AT3G14930   uroporphyrinogen decarboxylase 1
Candida albicans CaO19.5369   uroporphyrinogen decarboxylase
Candida albicans CaO19.12829   uroporphyrinogen decarboxylase
Chlamydia trachomatis CT_747   uroporphyrinogen decarboxylase
Dictyostelium discoideum DDB_G0292294   uroporphyrinogen decarboxylase
Drosophila melanogaster Dmel_CG1818   CG1818 gene product from transcript CG1818-RA
Escherichia coli b3997   uroporphyrinogen decarboxylase
Echinococcus granulosus EgrG_000492300   uroporphyrinogen decarboxylase
Echinococcus granulosus EgrG_000492200   uroporphyrinogen decarboxylase
Echinococcus multilocularis EmuJ_000492200   uroporphyrinogen decarboxylase
Echinococcus multilocularis EmuJ_000492300   uroporphyrinogen decarboxylase
Homo sapiens ENSG00000126088   uroporphyrinogen decarboxylase
Mycobacterium leprae ML1043   PROBABLE UROPORPHYRINOGEN DECARBOXYLASE HEME (UROPORPHYRINOGEN III DECARBOXYLASE) (URO-D) (UPD)
Mus musculus ENSMUSG00000028684   uroporphyrinogen decarboxylase
Mycobacterium tuberculosis Rv2678c   Probable uroporphyrinogen decarboxylase HemE (uroporphyrinogen III decarboxylase) (URO-D) (UPD)
Mycobacterium ulcerans MUL_3312   uroporphyrinogen decarboxylase
Neospora caninum NCLIV_042300   Uroporphyrinogen decarboxylase (EC 4.1.1.37), related
Oryza sativa 9268639   Os03g0340001
Oryza sativa 4332771   Os03g0337600
Oryza sativa 4326635   Os01g0622300
Plasmodium berghei PBANKA_0105900   uroporphyrinogen III decarboxylase
Plasmodium falciparum PF3D7_0607300   uroporphyrinogen III decarboxylase
Plasmodium knowlesi PKNH_1143000   uroporphyrinogen III decarboxylase, putative
Plasmodium vivax PVX_113530   uroporphyrinogen III decarboxylase, putative
Plasmodium yoelii PY02528   uroporphyrinogen decarboxylase, putative
Saccharomyces cerevisiae YDR047W   uroporphyrinogen decarboxylase HEM12
Schistosoma japonicum Sjp_0084260   ko:K01599 uroporphyrinogen decarboxylase [EC4.1.1.37], putative
Schistosoma mansoni Smp_143740   uroporphyrinogen decarboxylase
Schmidtea mediterranea mk4.002378.01   Uroporphyrinogen decarboxylase
Schmidtea mediterranea mk4.044698.00   Uroporphyrinogen decarboxylase
Schmidtea mediterranea mk4.014694.00   Uroporphyrinogen decarboxylase
Toxoplasma gondii TGME49_289940   uroporphyrinogen decarboxylase
Wolbachia endosymbiont of Brugia malayi Wbm0001   uroporphyrinogen-III decarboxylase

Essentiality

PF3D7_0607300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3997 Escherichia coli essential goodall
YDR047W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0105900 Plasmodium berghei Dispensable plasmo
TGME49_289940 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Druggability index (range: 0 to 1): 0.1

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier PF3D7_0607300 (Plasmodium falciparum), uroporphyrinogen III decarboxylase
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